IGVFDS0319JZYS

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS0319JZYS/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS0319JZYS",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS0319JZYS](/auxiliary-sets/IGVFDS0319JZYS/) has sequence file(s) [IGVFFI3927LCXN](/sequence-files/IGVFFI3927LCXN/), [IGVFFI8797POIP](/sequence-files/IGVFFI8797POIP/), [IGVFFI4291ESKX](/sequence-files/IGVFFI4291ESKX/), [IGVFFI1384RCQE](/sequence-files/IGVFFI1384RCQE/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS0319JZYS/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG011972/",
        "component": "functional characterization",
        "contact_pi": {
            "@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
            "title": "Jesse Engreitz"
        },
        "title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
    },
    "control_for": [],
    "creation_timestamp": "2024-05-13T22:38:44.538418+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO0384OZRW/",
            "accession": "IGVFDO0384OZRW",
            "aliases": [
                "igvf:donor_of_HCT116"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "gRNA sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI3927LCXN/",
            "accession": "IGVFFI3927LCXN",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:35:55.762873+00:00",
            "file_format": "fastq",
            "file_size": 22496682,
            "href": "/sequence-files/IGVFFI3927LCXN/@@download/IGVFFI3927LCXN.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/dfc39d1a-e2e6-44b3-863e-d2f3b4958692/IGVFFI3927LCXN.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinA-PCR1-Rep1_S217_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7867OONC/",
            "accession": "IGVFFI7867OONC",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:27:58.294046+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI7867OONC/@@download/IGVFFI7867OONC.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/930f1b1a-12c6-4d25-9491-84f6828579cc/IGVFFI7867OONC.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8797POIP/",
            "accession": "IGVFFI8797POIP",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:36:14.278905+00:00",
            "file_format": "fastq",
            "file_size": 17334895,
            "href": "/sequence-files/IGVFFI8797POIP/@@download/IGVFFI8797POIP.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/d9548d5b-ab17-4c0b-a5f1-c8b0529d7616/IGVFFI8797POIP.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinA-PCR2-Rep1_S223_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4291ESKX/",
            "accession": "IGVFFI4291ESKX",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:36:32.542392+00:00",
            "file_format": "fastq",
            "file_size": 30283642,
            "href": "/sequence-files/IGVFFI4291ESKX/@@download/IGVFFI4291ESKX.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/b769cc3d-84cf-41f6-9373-6090410687f7/IGVFFI4291ESKX.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinA-PCR3-Rep1_S259_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1384RCQE/",
            "accession": "IGVFFI1384RCQE",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:36:50.518482+00:00",
            "file_format": "fastq",
            "file_size": 25189873,
            "href": "/sequence-files/IGVFFI1384RCQE/@@download/IGVFFI1384RCQE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/212cfb93-8307-4575-8e5e-083217bd59cf/IGVFFI1384RCQE.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinA-PCR4-Rep1_S265_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1446IYEI/",
            "accession": "IGVFFI1446IYEI",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:28:12.941557+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI1446IYEI/@@download/IGVFFI1446IYEI.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/1ff34b94-983c-44a7-b74f-1c3f9bf4f549/IGVFFI1446IYEI.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0717WSTW/",
            "accession": "IGVFFI0717WSTW",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:28:27.403902+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI0717WSTW/@@download/IGVFFI0717WSTW.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/5c6165a7-3847-4a1f-8f27-b75bc7601575/IGVFFI0717WSTW.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6982FUBD/",
            "accession": "IGVFFI6982FUBD",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:28:41.197659+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI6982FUBD/@@download/IGVFFI6982FUBD.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/bb8c1480-e476-44f4-b97a-283171c69696/IGVFFI6982FUBD.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS1569RNPD/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS6376TFTJ/",
            "accession": "IGVFDS6376TFTJ",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:07:50.695939+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM9315IOJD/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9315IOJD",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS6351FGNG/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                },
                {
                    "@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
                    "modality": "degradation",
                    "status": "released"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002824/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:HCT116"
                    ],
                    "status": "released",
                    "summary": "HCT116",
                    "term_name": "HCT116"
                }
            ],
            "status": "released",
            "summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin A for 0-10% expression of CCND1) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "12",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-01T01:35:55.762873+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "a9c09edc-8211-4f32-8341-8035c2aa8f46"
}